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Revision f318c828

IDf318c828821be9d6f4a5359c1f8e494140e3863e
Parent 5711e069
Child b3babf1b

Added by Katja Luther almost 4 years ago

ref #6314: handle homotypical group and further implementation for filling the name table

View differences:

cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/outputmodel/OutputModelClassificationExport.java
8 8 
*/
9 9 
package eu.etaxonomy.cdm.io.outputmodel;
10 10 

  		




  
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import java.util.ArrayList;


  		




  
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import java.util.Collections;


  		




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import java.util.Iterator;


  		




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import java.util.List;


  		




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import java.util.Set;


  		




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import java.util.UUID;


  		




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import org.apache.commons.lang3.StringUtils;


  		




  
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import eu.etaxonomy.cdm.common.CdmUtils;


  		




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import eu.etaxonomy.cdm.io.common.CdmExportBase;


  		




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import eu.etaxonomy.cdm.io.common.ICdmExport;


  		




  ......




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import eu.etaxonomy.cdm.model.media.Media;


  		




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import eu.etaxonomy.cdm.model.media.MediaRepresentation;


  		




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import eu.etaxonomy.cdm.model.media.MediaRepresentationPart;


  		




  
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;


  		




  
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import eu.etaxonomy.cdm.model.name.HomotypicalGroupNameComparator;


  		




  
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import eu.etaxonomy.cdm.model.name.NameTypeDesignation;


  		




  
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import eu.etaxonomy.cdm.model.name.NomenclaturalStatus;


  		




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import eu.etaxonomy.cdm.model.name.Rank;


  		




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import eu.etaxonomy.cdm.model.name.TaxonNameBase;


  		




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import eu.etaxonomy.cdm.model.reference.Reference;


  		




  ......




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        String[] csvLine = new String[table.getSize()];


  		




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        csvLine[table.getIndex(OutputModelTable.NAME_ID)] = getId(state, name);


  		




  
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        csvLine[table.getIndex(OutputModelTable.LSID)] = name.getLsid().getLsid();


  		




  
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        csvLine[table.getIndex(OutputModelTable.RANK)] = getTitleCache(rank);


  		




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        csvLine[table.getIndex(OutputModelTable.RANK_SEQUENCE)] = String.valueOf(rank.getOrderIndex());


  		




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        csvLine[table.getIndex(OutputModelTable.FULL_NAME_WITH_AUTHORS)] = getTropicosTitleCache(name);


  		




  ......




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        }else{


  		




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            csvLine[table.getIndex(OutputModelTable.PROTOLOGUE_URI)] = "";


  		




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        }


  		




  
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        if (name.getStatus() != null || name.getStatus().isEmpty()){


  		




  
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            csvLine[table.getIndex(OutputModelTable.NOM_STATUS)] = "";


  		




  
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            csvLine[table.getIndex(OutputModelTable.NOM_STATUS_ABBREV)] = "";


  		




  
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        }else{


  		




  
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            String statusStringAbbrev = extractStatusString(name, true);


  		




  
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            String statusString = extractStatusString(name, false);


  		




  
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            csvLine[table.getIndex(OutputModelTable.NOM_STATUS)] = statusString.trim();


  		




  
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            csvLine[table.getIndex(OutputModelTable.NOM_STATUS_ABBREV)] = statusStringAbbrev.trim();


  		




  
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        }


  		




  
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        HomotypicalGroup group =name.getHomotypicalGroup();


  		




  
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        if (state.getHomotypicalGroupFromStore(group.getId()) == null){


  		




  
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            handleHomotypicalGroup(state, group);


  		




  
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        }


  		




  
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        csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_FK)] = String.valueOf(group.getId());


  		




  
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        //csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_FK)] = String.valueOf(group.getTypifiedNames());


  		




  
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        state.getProcessor().put(table, name, csvLine);


  		




  
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        state.getProcessor().put(table, name, csvLine);


  		




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/*


  		




  ......




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DatePublished


  		




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YearPublished


  		




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TitlePageYear


  		




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ProtologueURI


  		




  249
  
  
    
NomenclaturalStatus


  		




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NomenclaturalStatusAbbreviation


  		




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HomotypicGroup_Fk


  		




  
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HomotypicGroupSequenceNumber


  		




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TypeString


  		




  
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 *


  		




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 */


  		




  ......




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    /**


  		




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     * @param name


  		




  
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     * @param statusString


  		




  
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     * @return


  		




  
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     */


  		




  
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    private String extractStatusString(TaxonNameBase name, boolean abbrev) {


  		




  
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        Set<NomenclaturalStatus> status = name.getStatus();


  		




  
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        String statusString = "";


  		




  
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        for (NomenclaturalStatus nameStatus: status){


  		




  
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            if (abbrev){


  		




  
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                statusString += nameStatus.getType().getIdInVocabulary();


  		




  
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            }else{


  		




  
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                statusString += nameStatus.getType().getTitleCache();


  		




  
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            }


  		




  
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            if (!abbrev){


  		




  
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                if (!StringUtils.isBlank(nameStatus.getRuleConsidered())){


  		




  
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                    statusString += " " + nameStatus.getRuleConsidered();


  		




  
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                }


  		




  
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                if (nameStatus.getCitation() != null){


  		




  
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                    statusString += " " + nameStatus.getCitation().getTitleCache();


  		




  
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                }


  		




  
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                if (!StringUtils.isBlank(nameStatus.getCitationMicroReference())){


  		




  
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                    statusString += " " + nameStatus.getCitationMicroReference();


  		




  
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                }


  		




  
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            }


  		




  
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            statusString += " ";


  		




  
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        }


  		




  
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        return statusString;


  		




  
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    }


  		




  
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    /**


  		




  
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     * @param group


  		




  
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     */


  		




  
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    private void handleHomotypicalGroup(OutputModelExportState state, HomotypicalGroup group) {


  		




  
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        state.addHomotypicalGroupToStore(group);


  		




  
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        OutputModelTable table = OutputModelTable.HOMOTYPIC_GROUP;


  		




  
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        String[] csvLine = new String[table.getSize()];


  		




  
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        csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_ID)] = String.valueOf(group.getId());


  		




  
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        List<TaxonNameBase> typifiedNames = new ArrayList<>();


  		




  
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        typifiedNames.addAll(group.getTypifiedNames());


  		




  
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        Collections.sort(typifiedNames, new HomotypicalGroupNameComparator(null, true));


  		




  
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        String typifiedNamesString = "";


  		




  
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        for (TaxonNameBase name: typifiedNames){


  		




  
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            //Concatenated output string for homotypic group (names and citations) + status + some name relations (e.g. “non”)


  		




  
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//TODO: nameRelations, which and how to display


  		




  
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            typifiedNamesString = name.getTitleCache() + " " + extractStatusString(name, true) + " ";


  		




  
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        }


  		




  
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        csvLine[table.getIndex(OutputModelTable.HOMOTYPIC_GROUP_SEQ)] = typifiedNamesString.trim();


  		




  
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        Set<NameTypeDesignation> typeDesigantions = group.getNameTypeDesignations();


  		




  
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        for (NameTypeDesignation typeDesignation: typeDesigantions){


  		




  
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            //TODO...


  		




  
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        }


  		




  
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    }


  		




  
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    /**


  		




  
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     * @param name


  		




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     * @return


  		




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     */


  		




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    private String getTropicosTitleCache(TaxonNameBase name) {


  		












  

    
      cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/outputmodel/OutputModelExportState.java
    
  





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*/


  		




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package eu.etaxonomy.cdm.io.outputmodel;


  		




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import java.util.HashMap;


  		




  
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import java.util.Map;


  		




  
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import eu.etaxonomy.cdm.io.common.ExportResult;


  		




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import eu.etaxonomy.cdm.io.common.ExportResult.ExportResultState;


  		




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import eu.etaxonomy.cdm.io.common.ExportStateBase;


  		




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import eu.etaxonomy.cdm.io.common.mapping.out.IExportTransformer;


  		




  
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import eu.etaxonomy.cdm.model.name.HomotypicalGroup;


  		




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import eu.etaxonomy.cdm.model.taxon.TaxonBase;


  		




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/**


  		




  ......




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    private TaxonBase actualTaxonBase;


  		




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    private Map<Integer, HomotypicalGroup> homotypicalGroupStore = new HashMap<Integer, HomotypicalGroup>();


  		




  
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    /**


  		




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     * @param config


  		




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     */


  		




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    protected OutputModelExportState(OutputModelConfigurator config) {


  		




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        super(config);


  		




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        result = ExportResult.NewInstance(config.getResultType());


  		




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    }


  		




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    /**


  		




  ......




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    public TaxonBase getActualTaxonBase() {return actualTaxonBase;}


  		




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    /**


  		




  
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     * @return the homotypicalGroupStore


  		




  
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     */


  		




  
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    public Map<Integer, HomotypicalGroup> getHomotypicalGroupStore() {


  		




  
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        return homotypicalGroupStore;


  		




  
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    }


  		




  
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    /**


  		




  
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     * @param homotypicalGroupStore the homotypicalGroupStore to set


  		




  
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     */


  		




  
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    public void addHomotypicalGroupToStore(HomotypicalGroup homotypicalGroup) {


  		




  
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        this.homotypicalGroupStore.put(homotypicalGroup.getId(), homotypicalGroup);


  		




  
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    }


  		




  
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    public HomotypicalGroup getHomotypicalGroupFromStore(Integer id){


  		




  
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        return homotypicalGroupStore.get(id);


  		




  
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    }


  		




  
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}


  		












  

    
      cdmlib-io/src/main/java/eu/etaxonomy/cdm/io/outputmodel/OutputModelTable.java
    
  





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    protected static final String NAME_ID = "Name_ID";


  		




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    protected static final String TROPICOS_ID = "Tropicos_ID";


  		




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    protected static final String IPNI_ID = "IPNI_ID";


  		




  
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    protected static final String LSID = "LSID";


  		




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    protected static final String RANK = "Rank";


  		




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    protected static final String RANK_SEQUENCE = "Name_ID";


  		




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    protected static final String FULL_NAME_WITH_AUTHORS = "FullNameWithAuthors";


  		












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